Scientists come up with National Genomic Atlas to aid in Listeria tracking

U.S – Cornell University food scientists have created a new genomic and geological mapping tool that may soon prove Listeria monocytogenes, one of the most noxious foodborne pathogens, easier to track down in food recalls and other investigations.

The national atlas will inform scientists on the residence of listeria and other related species within the contiguous United States, which could help them trace and pinpoint sources of listeria found in ingredients, food processing facilities, and finished products, according to research published in Nature Microbiology.

“As we’re trying to figure out the risk of getting listeria from soil and different locations, our group created a more systematic way of assessing how frequently different listeria are found in different locations. We’ve studied listeria in places as diverse as New York, Colorado, and California, but before this atlas, it was difficult to make comparisons and assess listeria diversity in different locations,” said senior author Martin Wiedmann, food safety and food science professor in the College of Agriculture and Life Sciences.

Listeriosis is a serious infection usually caused by eating food contaminated with the bacterium Listeria monocytogenes. The Centers for Disease Control and Prevention (CDC) estimate that 1,600 people get listeriosis each year, and about 260 die. The infection is most likely to sicken pregnant women and their newborns, adults aged 65 or older, and people with weakened immune systems.

Cognizant that listeria occurs naturally in soil, the Cornell group requested hundreds of other scientists across the country to scoop up soil samples from generally undisturbed places in the natural world, such as the off-trail areas of state and national parks.

The group developed a nationwide atlas of 1,854 listeria isolates, representing 594 strains and 12 families of the bacteria called phylogroups from these samples.

Lead author Jingqiu Liao, who worked in Wiedmann’s laboratory as a graduate student, and now a post-doctoral researcher at Columbia University, supplemented the research by acquiring soil samples in her own travels and found listeria present across a wide range of environmental circumstances.

This bacterium is controlled mainly by soil moisture, salinity concentrations, and molybdenum—a trace mineral found in milk, cheese, grains, legumes, leafy vegetables, and organ meats.

“The goal of this work was to systematically collect soil samples across the U.S, and to capture the true large-scale spatial distribution, genomic diversity, and population structure of listeria species in the natural environment,” said Liao.

Liao enlightened that they provided answers to the ecological and evolutionary drivers of bacterial genome flexibility – an important open question in the field of microbiology – with whole genome sequencing and comprehensive population genomics analyses.

He explicated that this work can serve as a reference for future population genomics studies and will likely benefit the food industry by locating listeria contaminations that may have a natural origin.

“If listeria is found in a processing facility in the western US, for example, and that facility had used ingredients from a distant state, knowing the genomic information of listeria isolates and their possible locations across the U.S, we can better narrow the origins to a specific region. You can use this information almost like a traceback. It’s not always proof, but it leads you to evidence,” said Wiedmann.

Besides Wiedmann and Liao, the other authors of the atlas titled, “Nationwide Genomic Atlas of Soil-Dwelling Listeria Reveals Effects of Selection and Population Ecology on Pangenome Evolution,” are Daniel Buckley, professor of microbial ecology in the School of Integrative Plant Science Soil and Crop Sciences Section; Otto Cordero, associate professor of civil and environmental engineering, Massachusetts Institute of Technology (MIT); Shaul Pollak, postdoctoral researcher, MIT; Daniel Weller, Cornell researcher, CDC; and Sean (Xiaodong) Guo, Cornell research technician.

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